Hi:
This is really a question for Tech Support. In the glossary
(
http://support.sas.com/rnd/itech/doc9/glossary.html#C ), it says that "A custom repository is used to specify resources that are unique to a particular data collection." I believe -which- resources are available depend on your configuration, security and server setup.
There are SAS solutions, such as ITRM, that run in a custom repository and have stored processes. I am not sure where the stored processes "live" -- in the Foundation repository, or in the custom repository.
I really think you should contact Tech Support to open a ticket about this question. When you are building the architecture for an application or solution, it is better to get the final word on what's possible or not from Tech Support -- because if they do not know the answer to your question, they have the resources to get the definitive answer to your question.
cynthia